Goal of this document is to review the Feather River redd data and understand the following:

Relevant Science Plan hypotheses

  1. Spawning habitat acreage
  1. Salmon redd density (this is the most relevant hypothesis)
  1. Natural origin adult Chinook salmon population estimates by tributary, and trend in abundance (harvest plus escapement)

Contact

These data were originally acquired from Chris Cook

Timeframe

Data quality

Data questions

  • Latitude/Longitude unit system is inconsistent. Only 2023 has UTM coordinate system, other years following are shown as “latitude mn / longitude me” (probably zone 10). This is some information we have found about that coordinate system. Why were the coordinate systems different?
  • 2023 data has 6 fields for types of soil (boulder, cobble, pebble, gravel, sand and silt), other years have 5 (fines, small, med, large). They were matched by size but % silt was left out for now. Should we include that column in combined data?
  • 2014-10-20 has 6 records with high number_salmon numbers (over 15, check if these are not errors)
  • Velocity on 2020-11–18 is negative, is it safe to assume this is a mistake, we turn these into NA
  • There are some pretty high pot_depth_m over 40, is it safe to assume this is a mistake, we turn these into NA
  • There are five record values for number of salmon that are over 20 (2014-10-20), can we confirm these are accurate?

Combining all years into one object

## Rows: 36,876
## Columns: 22
## $ date            <date> 2014-09-09, 2014-09-09, 2014-09-15, 2014-09-15, 2014-…
## $ survey_wk       <chr> "1-1", "1-1", "2-1", "2-1", "2-1", "2-1", "2-1", "2-1"…
## $ location        <chr> "moe's side channel", "upper cottonwood", "cottonwood"…
## $ file_number     <dbl> 1, 2, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 1…
## $ type            <chr> "p", "p", "p", "p", "p", "p", "p", "p", "p", "p", "p",…
## $ number_redds    <dbl> 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, …
## $ number_salmon   <dbl> 1, 1, 1, 0, 3, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 1, …
## $ depth_m         <dbl> 0.30, 0.62, NA, NA, NA, NA, NA, NA, NA, NA, NA, 0.72, …
## $ pot_depth_m     <dbl> 0.50, 0.70, NA, NA, NA, NA, NA, NA, NA, NA, NA, 0.76, …
## $ velocity_m_s    <dbl> 0.61, 0.89, NA, NA, NA, NA, NA, NA, NA, NA, NA, 0.55, …
## $ percent_fines   <dbl> 40, 0, NA, NA, NA, NA, NA, NA, NA, NA, NA, 0, 0, 0, 0,…
## $ percent_small   <dbl> 20, 65, NA, NA, NA, NA, NA, NA, NA, NA, NA, 40, 40, 60…
## $ percent_med     <dbl> 35, 30, NA, NA, NA, NA, NA, NA, NA, NA, NA, 50, 60, 20…
## $ percent_large   <dbl> 5, 5, NA, NA, NA, NA, NA, NA, NA, NA, NA, 10, 0, 10, 0…
## $ percent_boulder <dbl> 0, 0, NA, NA, NA, NA, NA, NA, NA, NA, NA, 0, 0, 10, 0,…
## $ redd_width_m    <dbl> 1.1, 2.5, NA, NA, NA, NA, NA, NA, NA, NA, NA, 1.5, 2.0…
## $ redd_length_m   <dbl> 2.0, 3.5, NA, NA, NA, NA, NA, NA, NA, NA, NA, 2.0, 2.5…
## $ longitude       <dbl> 0.0000, -121.5542, -121.5558, -121.5557, -121.5556, -1…
## $ latitude        <dbl> 0.00000, 39.51675, 39.51665, 39.51663, 39.51666, 39.51…
## $ elevation_ft    <dbl> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…
## $ accuracy_ft     <dbl> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…
## $ boat_point      <lgl> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…

Data exploration

Exploring fields that have data consistently

date

  • Surveys are conducted September to December
## [1] "2014-09-09" "2023-11-29"

Looking at temporal coverage

Since there are outliers, will remove and plot again

location

  • Location clean up is needed. There are some names that appear less than 5 times. We could check if they correspond to another location name, and it is spelled differently
## 
##                         aleck                  aleck riffle 
##                            90                            32 
##                       bedrock                bedrock riffle 
##                           898                          1982 
##           below big hole east        below lower auditorium 
##                            59                           481 
##                       big bar                big bar riffle 
##                            33                            24 
##                 big hole east                 big hole west 
##                           274                            47 
##                    big riffle                    cottonwood 
##                           104                          1214 
##                    developing             developing riffle 
##                             4                             3 
##                           eye              eye side channel 
##                            42                           107 
## g-95 east side channel bottom                 g-95 east top 
##                             1                             1 
##                     g-95 main g-95 west side channel bottom 
##                             1                             1 
##               g95 east bottom  g95 east side channel bottom 
##                           137                            66 
##     g95 east side channel top                  g95 east top 
##                            34                           103 
##                      g95 main                      g95 west 
##                            67                            40 
##               g95 west bottom         g95 west side channel 
##                             1                            23 
##                       gateway          gateway main channel 
##                            42                            15 
##          gateway side channel                         goose 
##                             8                            22 
##                  goose riffle                 great western 
##                             7                             7 
##                      hatchery                 hatchery pipe 
##                          1594                           892 
##               hatchery riffle         hatchery side channel 
##                          2169                           136 
##   hatchery side channel upper                     high flow 
##                             1                             1 
##                          hour                       keister 
##                            35                           105 
##              lower auditorium              lower big riffle 
##                          6052                             8 
##                    lower hour               lower mcfarland 
##                           225                            31 
##                lower robinson          lower table mountain 
##                           998                           912 
##              lower vance east                       mathews 
##                            35                           190 
##                      matthews                mid auditorium 
##                            75                           102 
##                      mid hour             middle auditorium 
##                            12                          1483 
##                   moe's ditch            moe's side channel 
##                            65                          2608 
##                          palm                   palm riffle 
##                             4                             1 
##                         steep                  steep riffle 
##                            92                           146 
##                    steep side            steep side channel 
##                            54                            98 
##                table mountain             top of auditorium 
##                          1050                          3588 
##              top of audtorium               top of hatchery 
##                           318                             9 
##                  trailer park              upper auditorium 
##                          1607                          2313 
##           upper big hole east              upper cottonwood 
##                             2                           644 
##                upper hatchery         upper hatchery riffle 
##                           696                           909 
##                    upper hour               upper hour east 
##                            99                             2 
##                 upper mathews                upper matthews 
##                           134                            33 
##               upper mcfarland                upper robinson 
##                            38                           843 
##                    vance east                    vance west 
##                           169                            50 
##                          weir                   weir riffle 
##                           105                           168
##  [1] "moe's side channel"            "upper cottonwood"             
##  [3] "cottonwood"                    "lower auditorium"             
##  [5] "top of auditorium"             "upper hatchery riffle"        
##  [7] "upper auditorium"              "mid auditorium"               
##  [9] "hatchery riffle"               "developing riffle"            
## [11] "upper mcfarland"               "big riffle"                   
## [13] "g95 east bottom"               "g95 main"                     
## [15] "big hole east"                 "vance east"                   
## [17] "below big hole east"           "upper hour east"              
## [19] "upper hour"                    "mid hour"                     
## [21] "keister"                       "big bar"                      
## [23] "lower mcfarland"               "middle auditorium"            
## [25] "upper hatchery"                "hatchery"                     
## [27] "hatchery side channel"         "table mountain"               
## [29] "goose"                         "g95 west side channel"        
## [31] "upper big hole east"           "g95 east side channel bottom" 
## [33] "g-95 east top"                 "g-95 main"                    
## [35] "lower hour"                    "hour"                         
## [37] "g95 east side channel top"     "developing"                   
## [39] "moe's ditch"                   "lower robinson"               
## [41] "trailer park"                  "mathews"                      
## [43] "g-95 east side channel bottom" "g-95 west side channel bottom"
## [45] "upper robinson"                "weir riffle"                  
## [47] "steep riffle"                  "eye side channel"             
## [49] "steep side channel"            "aleck"                        
## [51] "lower vance east"              "vance west"                   
## [53] "g95 east top"                  "upper mathews"                
## [55] "great western"                 "lower table mountain"         
## [57] "top of hatchery"               "bedrock"                      
## [59] "hatchery pipe"                 "steep"                        
## [61] "below lower auditorium"        "big hole west"                
## [63] "lower big riffle"              "weir"                         
## [65] "eye"                           "gateway"                      
## [67] "g95 west"                      "palm"                         
## [69] NA                              "matthews"                     
## [71] "high flow"                     "upper matthews"               
## [73] "bedrock riffle"                "aleck riffle"                 
## [75] "gateway side channel"          "gateway main channel"         
## [77] "goose riffle"                  "palm riffle"                  
## [79] "g95 west bottom"               "top of audtorium"             
## [81] "hatchery side channel upper"   "big bar riffle"               
## [83] "steep side"

Locations surveyed less than 5 times

For locations that are being surveyed less than five times, we might want to verify if they belong to other location area names. Otherwise, these sites might not have enough data to reliably analyze over time.

Frequent locations and years surveyed

type

Observations by type and date

## [1] "p" "a" NA

Count of observations by type

  • note that all 2023 data does not have a type field
  • based on conversations with the Feather River team we should remove the “a” observations and this field

redd_count

Redd counts by year

## [1]  0 15
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##   0.000   1.000   1.000   1.002   1.000  15.000

Same plot than above but with date values aggregated - using geom_col()

salmon_count

Salmon counts by year

  • Noticed some outliers. Plotting below again removing values over 20
## [1]  0 50
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max.    NA's 
##   0.000   0.000   0.000   0.297   0.000  50.000    6327

depth

## [1] 0.0 1.5
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max.    NA's 
##    0.00    0.32    0.44    0.45    0.56    1.50   31807

##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max.    NA's 
##    0.00    0.32    0.44    0.45    0.56    1.50   31807

velocity

## [1] -0.013  2.740
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max.    NA's 
##   -0.01    0.33    0.48    0.52    0.66    2.74   32903

Turning that negative velocity to NA and plotting

pot_depth_m

## [1] NA NA
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max.    NA's 
##    0.00    0.42    0.51    0.55    0.63   50.00   32197

Same plot as above but outliers removed

Turning values over 40 to NA

latitude/ longitude plot

Cleaning lat/long to plot on a map

summary of depth

##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max.    NA's 
##    0.00    0.32    0.44    0.45    0.56    1.50   31807

summary of pot_depth after modifications

##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max.    NA's 
##    0.00    0.42    0.51    0.53    0.63    1.70   32199

summary of velocity_m_s after modifications

##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max.    NA's 
##    0.00    0.33    0.48    0.52    0.66    2.74   32904

Plotting survey locations from Chris’ map

The following layers are included on map:

##  [1] "UpperHatchery"            "UpperCottonwood"         
##  [3] "Hatchery"                 "Cottonwood"              
##  [5] "TopofAuditorium"          "MoesSideChannel"         
##  [7] "UpperAuditorium"          "MiddleAuditorium"        
##  [9] "LowerAuditorium"          "HatcheryPipe"            
## [11] "LowerTableMountain"       "TableMountain"           
## [13] "BelowLowerAuditorium"     "Bedrock"                 
## [15] "TrailerPark"              "UpperMathews"            
## [17] "Mathews"                  "UpperRobinson"           
## [19] "LowerRobinson"            "Steep"                   
## [21] "SteepSideChannel"         "Weir"                    
## [23] "Eye"                      "EyeSideChannel"          
## [25] "Gateway"                  "Aleck"                   
## [27] "HatcherySideChannel"      "VanceEast"               
## [29] "VanceWest"                "BigHoleEast"             
## [31] "BigHoleWest"              "BelowBigHoleEast"        
## [33] "G95WestSideChannel"       "G95EastSideChannelTop"   
## [35] "G95EastSideChannelBottom" "UpperHour"               
## [37] "LowerHour"                "Keister"                 
## [39] "Goose"                    "Big"                     
## [41] "LowerBig"                 "BigBar"                  
## [43] "UpperMcFarland"           "LowerMcFarland"          
## [45] "Developing"

Adding the points where redds are found to the survey locations

#TODO (1) redd points that are off survey locations (2) locations per year that did not have redds